NM_001083962.2(TCF4):c.1089T>C (p.Ser363=) AND Pitt-Hopkins syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Oct 13, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001476494.14

Allele description [Variation Report for NM_001083962.2(TCF4):c.1089T>C (p.Ser363=)]

NM_001083962.2(TCF4):c.1089T>C (p.Ser363=)

Gene:

TCF4:transcription factor 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18q21.2

Genomic location:

Preferred name:

NM_001083962.2(TCF4):c.1089T>C (p.Ser363=)

HGVS:

NC_000018.10:g.55257372A>G
NG_011716.2:g.383622T>C
NM_001083962.2:c.1089T>CMANE SELECT
NM_001243226.3:c.1395T>C
NM_001243227.2:c.1017T>C
NM_001243228.2:c.1107T>C
NM_001243230.2:c.1080T>C
NM_001243231.2:c.963T>C
NM_001243232.1:c.876T>C
NM_001243233.2:c.699T>C
NM_001243234.2:c.609T>C
NM_001243235.2:c.609T>C
NM_001243236.2:c.609T>C
NM_001306207.1:c.1017T>C
NM_001306208.1:c.876T>C
NM_001330604.3:c.1086T>C
NM_001330605.3:c.699T>C
NM_001348211.2:c.963T>C
NM_001348212.2:c.699T>C
NM_001348213.2:c.699T>C
NM_001348214.2:c.606T>C
NM_001348215.2:c.441T>C
NM_001348216.2:c.609T>C
NM_001348217.1:c.1017T>C
NM_001348218.2:c.1017T>C
NM_001348219.2:c.1017T>C
NM_001348220.1:c.1014T>C
NM_001369567.1:c.1089T>C
NM_001369568.1:c.1089T>C
NM_001369569.1:c.1086T>C
NM_001369570.1:c.1086T>C
NM_001369571.1:c.1089T>C
NM_001369572.1:c.1089T>C
NM_001369573.1:c.1086T>C
NM_001369574.1:c.1086T>C
NM_001369575.1:c.1017T>C
NM_001369576.1:c.1014T>C
NM_001369577.1:c.1014T>C
NM_001369578.1:c.1014T>C
NM_001369579.1:c.1014T>C
NM_001369580.1:c.1014T>C
NM_001369581.1:c.1014T>C
NM_001369582.1:c.1017T>C
NM_001369583.1:c.1017T>C
NM_001369584.1:c.1014T>C
NM_001369585.1:c.1014T>C
NM_001369586.1:c.1020T>C
NM_003199.3:c.1089T>C
NP_001077431.1:p.Ser363=
NP_001230155.2:p.Ser465=
NP_001230156.1:p.Ser339=
NP_001230157.1:p.Ser369=
NP_001230159.1:p.Ser360=
NP_001230160.1:p.Ser321=
NP_001230161.1:p.Ser292=
NP_001230162.1:p.Ser233=
NP_001230163.1:p.Ser203=
NP_001230164.1:p.Ser203=
NP_001230165.1:p.Ser203=
NP_001293136.1:p.Ser339=
NP_001293137.1:p.Ser292=
NP_001317533.1:p.Ser362=
NP_001317534.1:p.Ser233=
NP_001335140.1:p.Ser321=
NP_001335141.1:p.Ser233=
NP_001335142.1:p.Ser233=
NP_001335143.1:p.Ser202=
NP_001335144.1:p.Ser147=
NP_001335145.1:p.Ser203=
NP_001335146.1:p.Ser339=
NP_001335147.1:p.Ser339=
NP_001335148.1:p.Ser339=
NP_001335149.1:p.Ser338=
NP_001356496.1:p.Ser363=
NP_001356497.1:p.Ser363=
NP_001356498.1:p.Ser362=
NP_001356499.1:p.Ser362=
NP_001356500.1:p.Ser363=
NP_001356501.1:p.Ser363=
NP_001356502.1:p.Ser362=
NP_001356503.1:p.Ser362=
NP_001356504.1:p.Ser339=
NP_001356505.1:p.Ser338=
NP_001356506.1:p.Ser338=
NP_001356507.1:p.Ser338=
NP_001356508.1:p.Ser338=
NP_001356509.1:p.Ser338=
NP_001356510.1:p.Ser338=
NP_001356511.1:p.Ser339=
NP_001356512.1:p.Ser339=
NP_001356513.1:p.Ser338=
NP_001356514.1:p.Ser338=
NP_001356515.1:p.Ser340=
NP_003190.1:p.Ser363=
NC_000018.9:g.52924603A>G
NM_001083962.1:c.1089T>C

Links:

dbSNP: rs1600406773

NCBI 1000 Genomes Browser:

rs1600406773

Molecular consequence:

NM_001083962.2:c.1089T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243226.3:c.1395T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243227.2:c.1017T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243228.2:c.1107T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243230.2:c.1080T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243231.2:c.963T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243232.1:c.876T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243233.2:c.699T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243234.2:c.609T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243235.2:c.609T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243236.2:c.609T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001306207.1:c.1017T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001306208.1:c.876T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001330604.3:c.1086T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001330605.3:c.699T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001348211.2:c.963T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001348212.2:c.699T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001348213.2:c.699T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001348214.2:c.606T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001348215.2:c.441T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001348216.2:c.609T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001348217.1:c.1017T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001348218.2:c.1017T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001348219.2:c.1017T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001348220.1:c.1014T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369567.1:c.1089T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369568.1:c.1089T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369569.1:c.1086T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369570.1:c.1086T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369571.1:c.1089T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369572.1:c.1089T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369573.1:c.1086T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369574.1:c.1086T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369575.1:c.1017T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369576.1:c.1014T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369577.1:c.1014T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369578.1:c.1014T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369579.1:c.1014T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369580.1:c.1014T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369581.1:c.1014T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369582.1:c.1017T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369583.1:c.1017T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369584.1:c.1014T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369585.1:c.1014T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369586.1:c.1020T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_003199.3:c.1089T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Pitt-Hopkins syndrome (PTHS)
Synonyms:: ENCEPHALOPATHY, SEVERE EPILEPTIC, WITH AUTONOMIC DYSFUNCTION; MENTAL RETARDATION, SYNDROMAL, WITH INTERMITTENT HYPERVENTILATION; Mental retardation, wide mouth, distinctive facial features, and intermittent hyperventilation followed by apnea
Identifiers:: MONDO: MONDO:0012589; MedGen: C1970431; Orphanet: 2896; OMIM: 610954

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LOC100820889 [Brachypodium distachyon]
LOC100820889 [Brachypodium distachyon]
Gene ID:100820889

Gene
LOC110487870 [Oncorhynchus mykiss]
LOC110487870 [Oncorhynchus mykiss]
Gene ID:110487870

Gene
peroxisome biogenesis factor 2 [Mus musculus]
peroxisome biogenesis factor 2 [Mus musculus]
gi|254028178|ref|NP_001156778.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001680703	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Oct 13, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001680703

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Oct 13, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001680703.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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